Job ID = 6366278 SRX = SRX105312 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:53:15 prefetch.2.10.7: 1) Downloading 'SRR363999'... 2020-06-15T22:53:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:55:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:55:10 prefetch.2.10.7: 1) 'SRR363999' was downloaded successfully Read 29041160 spots for SRR363999/SRR363999.sra Written 29041160 spots for SRR363999/SRR363999.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:03:53 29041160 reads; of these: 29041160 (100.00%) were unpaired; of these: 10749448 (37.01%) aligned 0 times 15214353 (52.39%) aligned exactly 1 time 3077359 (10.60%) aligned >1 times 62.99% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1906681 / 18291712 = 0.1042 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:04:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:04:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:34: 1000000 INFO @ Tue, 16 Jun 2020 08:04:40: 2000000 INFO @ Tue, 16 Jun 2020 08:04:46: 3000000 INFO @ Tue, 16 Jun 2020 08:04:52: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:04:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:04:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:59: 5000000 INFO @ Tue, 16 Jun 2020 08:05:04: 1000000 INFO @ Tue, 16 Jun 2020 08:05:06: 6000000 INFO @ Tue, 16 Jun 2020 08:05:10: 2000000 INFO @ Tue, 16 Jun 2020 08:05:13: 7000000 INFO @ Tue, 16 Jun 2020 08:05:16: 3000000 INFO @ Tue, 16 Jun 2020 08:05:19: 8000000 INFO @ Tue, 16 Jun 2020 08:05:22: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:05:26: 9000000 INFO @ Tue, 16 Jun 2020 08:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:05:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:29: 5000000 INFO @ Tue, 16 Jun 2020 08:05:33: 10000000 INFO @ Tue, 16 Jun 2020 08:05:34: 1000000 INFO @ Tue, 16 Jun 2020 08:05:35: 6000000 INFO @ Tue, 16 Jun 2020 08:05:40: 11000000 INFO @ Tue, 16 Jun 2020 08:05:40: 2000000 INFO @ Tue, 16 Jun 2020 08:05:41: 7000000 INFO @ Tue, 16 Jun 2020 08:05:46: 12000000 INFO @ Tue, 16 Jun 2020 08:05:46: 3000000 INFO @ Tue, 16 Jun 2020 08:05:47: 8000000 INFO @ Tue, 16 Jun 2020 08:05:53: 4000000 INFO @ Tue, 16 Jun 2020 08:05:53: 13000000 INFO @ Tue, 16 Jun 2020 08:05:54: 9000000 INFO @ Tue, 16 Jun 2020 08:05:59: 5000000 INFO @ Tue, 16 Jun 2020 08:06:00: 14000000 INFO @ Tue, 16 Jun 2020 08:06:00: 10000000 INFO @ Tue, 16 Jun 2020 08:06:05: 6000000 INFO @ Tue, 16 Jun 2020 08:06:06: 11000000 INFO @ Tue, 16 Jun 2020 08:06:06: 15000000 INFO @ Tue, 16 Jun 2020 08:06:11: 7000000 INFO @ Tue, 16 Jun 2020 08:06:12: 12000000 INFO @ Tue, 16 Jun 2020 08:06:13: 16000000 INFO @ Tue, 16 Jun 2020 08:06:16: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:06:16: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:06:16: #1 total tags in treatment: 16385031 INFO @ Tue, 16 Jun 2020 08:06:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:06:16: #1 tags after filtering in treatment: 16385031 INFO @ Tue, 16 Jun 2020 08:06:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:17: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 08:06:17: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:17: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:06:17: #2 alternative fragment length(s) may be 1,28,550,598 bps INFO @ Tue, 16 Jun 2020 08:06:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.05_model.r WARNING @ Tue, 16 Jun 2020 08:06:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:17: #2 You may need to consider one of the other alternative d(s): 1,28,550,598 WARNING @ Tue, 16 Jun 2020 08:06:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:06:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:17: 8000000 INFO @ Tue, 16 Jun 2020 08:06:18: 13000000 INFO @ Tue, 16 Jun 2020 08:06:23: 9000000 INFO @ Tue, 16 Jun 2020 08:06:24: 14000000 INFO @ Tue, 16 Jun 2020 08:06:29: 10000000 INFO @ Tue, 16 Jun 2020 08:06:30: 15000000 INFO @ Tue, 16 Jun 2020 08:06:35: 11000000 INFO @ Tue, 16 Jun 2020 08:06:36: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:06:38: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:06:38: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:06:38: #1 total tags in treatment: 16385031 INFO @ Tue, 16 Jun 2020 08:06:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:06:38: #1 tags after filtering in treatment: 16385031 INFO @ Tue, 16 Jun 2020 08:06:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:40: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 08:06:40: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:40: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:06:40: #2 alternative fragment length(s) may be 1,28,550,598 bps INFO @ Tue, 16 Jun 2020 08:06:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.10_model.r WARNING @ Tue, 16 Jun 2020 08:06:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:40: #2 You may need to consider one of the other alternative d(s): 1,28,550,598 WARNING @ Tue, 16 Jun 2020 08:06:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:06:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:41: 12000000 INFO @ Tue, 16 Jun 2020 08:06:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:46: 13000000 INFO @ Tue, 16 Jun 2020 08:06:52: 14000000 INFO @ Tue, 16 Jun 2020 08:06:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:57: 15000000 INFO @ Tue, 16 Jun 2020 08:07:03: 16000000 INFO @ Tue, 16 Jun 2020 08:07:05: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:07:05: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:07:05: #1 total tags in treatment: 16385031 INFO @ Tue, 16 Jun 2020 08:07:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:07:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:05: #1 tags after filtering in treatment: 16385031 INFO @ Tue, 16 Jun 2020 08:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:06: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 08:07:06: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:06: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:07:06: #2 alternative fragment length(s) may be 1,28,550,598 bps INFO @ Tue, 16 Jun 2020 08:07:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.20_model.r WARNING @ Tue, 16 Jun 2020 08:07:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:06: #2 You may need to consider one of the other alternative d(s): 1,28,550,598 WARNING @ Tue, 16 Jun 2020 08:07:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:07:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX105312/SRX105312.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling